dgllife.utils.ACNN_graph_construction_and_featurization

dgllife.utils.ACNN_graph_construction_and_featurization(ligand_mol, protein_mol, ligand_coordinates, protein_coordinates, max_num_ligand_atoms=None, max_num_protein_atoms=None, neighbor_cutoff=12.0, max_num_neighbors=12, strip_hydrogens=False)[source]

Graph construction and featurization for Atomic Convolutional Networks for Predicting Protein-Ligand Binding Affinity.

Parameters

  • ligand_mol (rdkit.Chem.rdchem.Mol) – RDKit molecule instance.

  • protein_mol (rdkit.Chem.rdchem.Mol) – RDKit molecule instance.

  • ligand_coordinates (Float Tensor of shape (V1, 3)) – Atom coordinates in a ligand.

  • protein_coordinates (Float Tensor of shape (V2, 3)) – Atom coordinates in a protein.

  • max_num_ligand_atoms (int or None) – Maximum number of atoms in ligands for zero padding, which should be no smaller than ligand_mol.GetNumAtoms() if not None. If None, no zero padding will be performed. Default to None.

  • max_num_protein_atoms (int or None) – Maximum number of atoms in proteins for zero padding, which should be no smaller than protein_mol.GetNumAtoms() if not None. If None, no zero padding will be performed. Default to None.

  • neighbor_cutoff (float) – Distance cutoff to define ‘neighboring’. Default to 12.

  • max_num_neighbors (int) – Maximum number of neighbors allowed for each atom. Default to 12.

  • strip_hydrogens (bool) – Whether to exclude hydrogen atoms. Default to False.